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Showing metabocard for Pelargonidin 3-arabinoside (HMDB0301663)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-22 04:55:07 UTC
Update Date2021-09-22 04:55:07 UTC
HMDB IDHMDB0301663
Secondary Accession NumbersNone
Metabolite Identification
Common NamePelargonidin 3-arabinoside
DescriptionPelargonidin 3-arabinoside is a member of the class of compounds known as anthocyanidin-3-o-glycosides. Anthocyanidin-3-o-glycosides are phenolic compounds containing one anthocyanidin moiety which is O-glycosidically linked to a carbohydrate moiety at the C3-position. Pelargonidin 3-arabinoside is practically insoluble (in water) and a very weakly acidic compound (based on its pKa). Pelargonidin 3-arabinoside can be found in a number of food items such as gooseberry, strawberry, black elderberry, and blackcurrant, which makes pelargonidin 3-arabinoside a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0301663 (Pelargonidin 3-arabinoside)

Pelargonidin 3-O-arabinoside
  Mrv1652309231721032D          

 33 36  0  0  1  0            999 V2000
   -0.0380    2.8296    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    2.0945    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8974    2.7620    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5619    3.5157    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6674    1.3099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7351    0.4505    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  3  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4749    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4749    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6674    1.3099    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2508    1.8933    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4521    1.0550    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    2.0945    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0724    1.4270    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8974    2.7620    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  6  0  0  0
  3  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  1  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 17 18  2  0  0  0  0
 11 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
  9 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
 26 27  2  0  0  0  0
 21 27  1  0  0  0  0
  6 28  1  0  0  0  0
 28 29  1  1  0  0  0
 28 30  1  6  0  0  0
 28 31  1  0  0  0  0
  2 31  1  0  0  0  0
 31 32  1  6  0  0  0
 31 33  1  6  0  0  0
M  CHG  1  19   1
M  END
Download

3D MOL for HMDB0301663 (Pelargonidin 3-arabinoside)

HMDB0301663
     RDKit          3D
Pelargonidin 3-arabinoside
 48 51  0  0  0  0  0  0  0  0999 V2000
    5.7465   -1.8040    0.0442 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0509   -0.7804    0.6849 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5448   -0.9822    0.4695 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8082   -0.0139    1.0681 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0275    0.6623    0.1320 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7838    0.2638    0.1552 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4365   -0.1266    0.1780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6626   -1.5295    0.1796 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9134   -2.0811    0.2128 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1390   -3.4394    0.2162 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0961   -4.3291    0.1839 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4133   -3.9835    0.2521 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4866   -3.1242    0.2853 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7588   -3.6827    0.3210 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2659   -1.7731    0.2819 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0057   -1.2146    0.2466 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7774    0.0416    0.2429 O   0  0  0  0  0  3  0  0  0  0  0  0
   -1.5804    0.6418    0.2096 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6162    2.0866    0.2148 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7798    2.7228    0.6614 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8764    4.0972    0.6248 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8517    4.8846    0.1562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9272    6.2794    0.1109 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7184    4.2613   -0.2793 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6266    2.8712   -0.2409 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7933    0.4864   -1.1711 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8824    1.3260   -1.1612 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3143   -0.9160   -1.0188 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3973   -1.8984   -1.3624 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7011   -1.5102   -0.0389 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3846    0.1778    0.2328 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3084   -0.7433    1.7570 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2804   -1.9760    0.8930 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2148    1.7606    0.3883 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1708   -2.1920    0.1573 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1271   -4.1366    0.1569 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5578   -5.0671    0.2541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1901   -3.8861    1.2163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1320   -1.1075    0.3086 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6088    2.1370    1.0375 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7632    4.5955    0.9651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2774    6.7627   -0.6837 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1054    4.8578   -0.6537 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2744    2.4755   -0.6393 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1407    0.6143   -2.0532 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7759    2.1099   -0.5626 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2755   -1.0593   -1.5831 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6076   -2.7594   -0.9221 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10 12  1  0
 12 13  2  0
 13 14  1  0
 13 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 22 24  1  0
 24 25  2  0
  5 26  1  0
 26 27  1  0
 26 28  1  0
 28 29  1  0
 28  3  1  0
 18  7  1  0
 25 19  1  0
 16  9  1  0
  1 30  1  0
  2 31  1  0
  2 32  1  0
  3 33  1  1
  5 34  1  1
  8 35  1  0
 11 36  1  0
 12 37  1  0
 14 38  1  0
 15 39  1  0
 20 40  1  0
 21 41  1  0
 23 42  1  0
 24 43  1  0
 25 44  1  0
 26 45  1  6
 27 46  1  0
 28 47  1  6
 29 48  1  0
M  CHG  1  17   1
M  END
Download

3D SDF for HMDB0301663 (Pelargonidin 3-arabinoside)

Pelargonidin 3-O-arabinoside
  Mrv1652309231721032D          

 33 36  0  0  1  0            999 V2000
   -0.0380    2.8296    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    2.0945    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8974    2.7620    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5619    3.5157    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6674    1.3099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7351    0.4505    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  3  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4749    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4749    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6674    1.3099    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2508    1.8933    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4521    1.0550    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    2.0945    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0724    1.4270    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8974    2.7620    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  6  0  0  0
  3  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  1  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 17 18  2  0  0  0  0
 11 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
  9 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
 26 27  2  0  0  0  0
 21 27  1  0  0  0  0
  6 28  1  0  0  0  0
 28 29  1  1  0  0  0
 28 30  1  6  0  0  0
 28 31  1  0  0  0  0
  2 31  1  0  0  0  0
 31 32  1  6  0  0  0
 31 33  1  6  0  0  0
M  CHG  1  19   1
M  END
> <DATABASE_ID>
HMDB0301663

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@]1(CO)O[C@]([H])(OC2=CC3=C(O)C=C(O)C=C3[O+]=C2C2=CC=C(O)C=C2)[C@@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C20H18O9/c21-8-16-17(25)18(26)20(29-16)28-15-7-12-13(24)5-11(23)6-14(12)27-19(15)9-1-3-10(22)4-2-9/h1-7,16-18,20-21,25-26H,8H2,(H2-,22,23,24)/p+1/t16-,17-,18+,20+/m1/s1

> <INCHI_KEY>
BGOQMKHOLJPANL-XSYGEPLQSA-O

> <FORMULA>
C20H19O9

> <MOLECULAR_WEIGHT>
403.3595

> <EXACT_MASS>
403.102907206

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
48

> <JCHEM_AVERAGE_POLARIZABILITY>
39.24365650844571

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-{[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1lambda4-chromen-1-ylium

> <ALOGPS_LOGP>
1.62

> <JCHEM_LOGP>
1.3438999999999997

> <ALOGPS_LOGS>
-3.20

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
7.535854645669778

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.396818473384804

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9811524252368704

> <JCHEM_POLAR_SURFACE_AREA>
152.98000000000002

> <JCHEM_REFRACTIVITY>
108.31409999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.78e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-{[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1lambda4-chromen-1-ylium

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0301663 (Pelargonidin 3-arabinoside)

HMDB0301663
     RDKit          3D
Pelargonidin 3-arabinoside
 48 51  0  0  0  0  0  0  0  0999 V2000
    5.7465   -1.8040    0.0442 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0509   -0.7804    0.6849 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5448   -0.9822    0.4695 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8082   -0.0139    1.0681 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0275    0.6623    0.1320 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7838    0.2638    0.1552 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4365   -0.1266    0.1780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6626   -1.5295    0.1796 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9134   -2.0811    0.2128 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1390   -3.4394    0.2162 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0961   -4.3291    0.1839 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4133   -3.9835    0.2521 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4866   -3.1242    0.2853 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7588   -3.6827    0.3210 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2659   -1.7731    0.2819 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0057   -1.2146    0.2466 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7774    0.0416    0.2429 O   0  0  0  0  0  3  0  0  0  0  0  0
   -1.5804    0.6418    0.2096 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6162    2.0866    0.2148 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7798    2.7228    0.6614 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8764    4.0972    0.6248 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8517    4.8846    0.1562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9272    6.2794    0.1109 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7184    4.2613   -0.2793 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6266    2.8712   -0.2409 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7933    0.4864   -1.1711 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8824    1.3260   -1.1612 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3143   -0.9160   -1.0188 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3973   -1.8984   -1.3624 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7011   -1.5102   -0.0389 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3846    0.1778    0.2328 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3084   -0.7433    1.7570 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2804   -1.9760    0.8930 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2148    1.7606    0.3883 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1708   -2.1920    0.1573 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1271   -4.1366    0.1569 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5578   -5.0671    0.2541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1901   -3.8861    1.2163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1320   -1.1075    0.3086 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6088    2.1370    1.0375 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7632    4.5955    0.9651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2774    6.7627   -0.6837 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1054    4.8578   -0.6537 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2744    2.4755   -0.6393 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1407    0.6143   -2.0532 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7759    2.1099   -0.5626 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2755   -1.0593   -1.5831 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6076   -2.7594   -0.9221 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10 12  1  0
 12 13  2  0
 13 14  1  0
 13 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 22 24  1  0
 24 25  2  0
  5 26  1  0
 26 27  1  0
 26 28  1  0
 28 29  1  0
 28  3  1  0
 18  7  1  0
 25 19  1  0
 16  9  1  0
  1 30  1  0
  2 31  1  0
  2 32  1  0
  3 33  1  1
  5 34  1  1
  8 35  1  0
 11 36  1  0
 12 37  1  0
 14 38  1  0
 15 39  1  0
 20 40  1  0
 21 41  1  0
 23 42  1  0
 24 43  1  0
 25 44  1  0
 26 45  1  6
 27 46  1  0
 28 47  1  6
 29 48  1  0
M  CHG  1  17   1
M  END
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PDB for HMDB0301663 (Pelargonidin 3-arabinoside)

HEADER    PROTEIN                                 23-SEP-17   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Pelargonidin 3-O-arabinoside                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-SEP-17         0                                  
HETATM    1  H   UNK     0      -0.071   5.282   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0      -0.770   3.910   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.675   5.156   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.049   6.563   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      -1.246   2.445   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    7  H   UNK     0       1.372   0.841   0.000  0.00  0.00           H+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+1
HETATM   20  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -4.001  -5.390   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.246   2.445   0.000  0.00  0.00           C+0
HETATM   29  H   UNK     0       2.335   3.534   0.000  0.00  0.00           H+0
HETATM   30  O   UNK     0       2.711   1.969   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       0.770   3.910   0.000  0.00  0.00           C+0
HETATM   32  H   UNK     0      -0.135   2.664   0.000  0.00  0.00           H+0
HETATM   33  O   UNK     0       1.675   5.156   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    5   31                                             
CONECT    3    2    4                                                       
CONECT    4    3                                                            
CONECT    5    2    6                                                       
CONECT    6    5    7    8   28                                             
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   20                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   18                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   11   19                                                  
CONECT   19   18   20                                                       
CONECT   20   19    9   21                                                  
CONECT   21   20   22   27                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26   21                                                       
CONECT   28    6   29   30   31                                             
CONECT   29   28                                                            
CONECT   30   28                                                            
CONECT   31   28    2   32   33                                             
CONECT   32   31                                                            
CONECT   33   31                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   72    0
END
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3D PDB for HMDB0301663 (Pelargonidin 3-arabinoside)

COMPND    HMDB0301663
HETATM    1  O1  UNL     1       5.747  -1.804   0.044  1.00  0.00           O  
HETATM    2  C1  UNL     1       5.051  -0.780   0.685  1.00  0.00           C  
HETATM    3  C2  UNL     1       3.545  -0.982   0.470  1.00  0.00           C  
HETATM    4  O2  UNL     1       2.808  -0.014   1.068  1.00  0.00           O  
HETATM    5  C3  UNL     1       2.027   0.662   0.132  1.00  0.00           C  
HETATM    6  O3  UNL     1       0.784   0.264   0.155  1.00  0.00           O  
HETATM    7  C4  UNL     1      -0.436  -0.127   0.178  1.00  0.00           C  
HETATM    8  C5  UNL     1      -0.663  -1.530   0.180  1.00  0.00           C  
HETATM    9  C6  UNL     1      -1.913  -2.081   0.213  1.00  0.00           C  
HETATM   10  C7  UNL     1      -2.139  -3.439   0.216  1.00  0.00           C  
HETATM   11  O4  UNL     1      -1.096  -4.329   0.184  1.00  0.00           O  
HETATM   12  C8  UNL     1      -3.413  -3.983   0.252  1.00  0.00           C  
HETATM   13  C9  UNL     1      -4.487  -3.124   0.285  1.00  0.00           C  
HETATM   14  O5  UNL     1      -5.759  -3.683   0.321  1.00  0.00           O  
HETATM   15  C10 UNL     1      -4.266  -1.773   0.282  1.00  0.00           C  
HETATM   16  C11 UNL     1      -3.006  -1.215   0.247  1.00  0.00           C  
HETATM   17  O6  UNL     1      -2.777   0.042   0.243  1.00  0.00           O1+
HETATM   18  C12 UNL     1      -1.580   0.642   0.210  1.00  0.00           C  
HETATM   19  C13 UNL     1      -1.616   2.087   0.215  1.00  0.00           C  
HETATM   20  C14 UNL     1      -2.780   2.723   0.661  1.00  0.00           C  
HETATM   21  C15 UNL     1      -2.876   4.097   0.625  1.00  0.00           C  
HETATM   22  C16 UNL     1      -1.852   4.885   0.156  1.00  0.00           C  
HETATM   23  O7  UNL     1      -1.927   6.279   0.111  1.00  0.00           O  
HETATM   24  C17 UNL     1      -0.718   4.261  -0.279  1.00  0.00           C  
HETATM   25  C18 UNL     1      -0.627   2.871  -0.241  1.00  0.00           C  
HETATM   26  C19 UNL     1       2.793   0.486  -1.171  1.00  0.00           C  
HETATM   27  O8  UNL     1       3.882   1.326  -1.161  1.00  0.00           O  
HETATM   28  C20 UNL     1       3.314  -0.916  -1.019  1.00  0.00           C  
HETATM   29  O9  UNL     1       2.397  -1.898  -1.362  1.00  0.00           O  
HETATM   30  H1  UNL     1       6.701  -1.510  -0.039  1.00  0.00           H  
HETATM   31  H2  UNL     1       5.385   0.178   0.233  1.00  0.00           H  
HETATM   32  H3  UNL     1       5.308  -0.743   1.757  1.00  0.00           H  
HETATM   33  H4  UNL     1       3.280  -1.976   0.893  1.00  0.00           H  
HETATM   34  H5  UNL     1       2.215   1.761   0.388  1.00  0.00           H  
HETATM   35  H6  UNL     1       0.171  -2.192   0.157  1.00  0.00           H  
HETATM   36  H7  UNL     1      -0.127  -4.137   0.157  1.00  0.00           H  
HETATM   37  H8  UNL     1      -3.558  -5.067   0.254  1.00  0.00           H  
HETATM   38  H9  UNL     1      -6.190  -3.886   1.216  1.00  0.00           H  
HETATM   39  H10 UNL     1      -5.132  -1.107   0.309  1.00  0.00           H  
HETATM   40  H11 UNL     1      -3.609   2.137   1.038  1.00  0.00           H  
HETATM   41  H12 UNL     1      -3.763   4.595   0.965  1.00  0.00           H  
HETATM   42  H13 UNL     1      -2.277   6.763  -0.684  1.00  0.00           H  
HETATM   43  H14 UNL     1       0.105   4.858  -0.654  1.00  0.00           H  
HETATM   44  H15 UNL     1       0.274   2.476  -0.639  1.00  0.00           H  
HETATM   45  H16 UNL     1       2.141   0.614  -2.053  1.00  0.00           H  
HETATM   46  H17 UNL     1       3.776   2.110  -0.563  1.00  0.00           H  
HETATM   47  H18 UNL     1       4.276  -1.059  -1.583  1.00  0.00           H  
HETATM   48  H19 UNL     1       2.608  -2.759  -0.922  1.00  0.00           H  
CONECT    1    2   30
CONECT    2    3   31   32
CONECT    3    4   28   33
CONECT    4    5
CONECT    5    6   26   34
CONECT    6    7
CONECT    7    8    8   18
CONECT    8    9   35
CONECT    9   10   10   16
CONECT   10   11   12
CONECT   11   36
CONECT   12   13   13   37
CONECT   13   14   15
CONECT   14   38
CONECT   15   16   16   39
CONECT   16   17
CONECT   17   18   18
CONECT   18   19
CONECT   19   20   20   25
CONECT   20   21   40
CONECT   21   22   22   41
CONECT   22   23   24
CONECT   23   42
CONECT   24   25   25   43
CONECT   25   44
CONECT   26   27   28   45
CONECT   27   46
CONECT   28   29   47
CONECT   29   48
END
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SMILES for HMDB0301663 (Pelargonidin 3-arabinoside)

[H][C@]1(CO)O[C@]([H])(OC2=CC3=C(O)C=C(O)C=C3[O+]=C2C2=CC=C(O)C=C2)[C@@]([H])(O)[C@]1([H])O
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INCHI for HMDB0301663 (Pelargonidin 3-arabinoside)

InChI=1S/C20H18O9/c21-8-16-17(25)18(26)20(29-16)28-15-7-12-13(24)5-11(23)6-14(12)27-19(15)9-1-3-10(22)4-2-9/h1-7,16-18,20-21,25-26H,8H2,(H2-,22,23,24)/p+1/t16-,17-,18+,20+/m1/s1
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC20H19O9
Average Molecular Weight403.3595
Monoisotopic Molecular Weight403.102907206
IUPAC Name3-{[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1lambda4-chromen-1-ylium
Traditional Name3-{[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1lambda4-chromen-1-ylium
CAS Registry NumberNot Available
SMILES
[H][C@]1(CO)O[C@]([H])(OC2=CC3=C(O)C=C(O)C=C3[O+]=C2C2=CC=C(O)C=C2)[C@@]([H])(O)[C@]1([H])O
InChI Identifier
InChI=1S/C20H18O9/c21-8-16-17(25)18(26)20(29-16)28-15-7-12-13(24)5-11(23)6-14(12)27-19(15)9-1-3-10(22)4-2-9/h1-7,16-18,20-21,25-26H,8H2,(H2-,22,23,24)/p+1/t16-,17-,18+,20+/m1/s1
InChI KeyBGOQMKHOLJPANL-XSYGEPLQSA-O
Chemical Taxonomy
Description Belongs to the class of organic compounds known as flavonoid 3-o-p-coumaroyl glycosides. These are flavonoid 3-O-glycosides where the carbohydrate moiety is esterified with a p-coumaric acid. P-coumaric acid is an organic derivative of cinnamic acid, that carries a hydroxyl group at the 4-position of the benzene ring.
KingdomOrganic compounds
Super ClassPhenylpropanoids and polyketides
ClassFlavonoids
Sub ClassFlavonoid glycosides
Direct ParentFlavonoid 3-O-p-coumaroyl glycosides
Alternative Parents
Substituents
  • Flavonoid 3-o-6-p-coumaroyl-glycoside
  • Anthocyanin
  • Anthocyanidin-3-o-glycoside
  • Flavonoid-3-o-glycoside
  • 3p-methoxyflavonoid-skeleton
  • Hydroxyflavonoid
  • 4'-hydroxyflavonoid
  • 5-hydroxyflavonoid
  • 7-hydroxyflavonoid
  • Anthocyanidin
  • Hydroxycinnamic acid or derivatives
  • Coumaric acid or derivatives
  • Cinnamic acid or derivatives
  • Cinnamic acid ester
  • Glycosyl compound
  • O-glycosyl compound
  • Dimethoxybenzene
  • M-dimethoxybenzene
  • Methoxyphenol
  • 1-benzopyran
  • Benzopyran
  • Styrene
  • Anisole
  • Phenoxy compound
  • Phenol ether
  • Methoxybenzene
  • Catechol
  • Phenol
  • Fatty acid ester
  • 1-hydroxy-2-unsubstituted benzenoid
  • 1-hydroxy-4-unsubstituted benzenoid
  • Alkyl aryl ether
  • Fatty acyl
  • Benzenoid
  • Monocyclic benzene moiety
  • Oxane
  • Monosaccharide
  • Heteroaromatic compound
  • Alpha,beta-unsaturated carboxylic ester
  • Enoate ester
  • Secondary alcohol
  • Carboxylic acid ester
  • Monocarboxylic acid or derivatives
  • Acetal
  • Polyol
  • Ether
  • Oxacycle
  • Organoheterocyclic compound
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Alcohol
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Organic cation
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP1.62ALOGPS
logP1.34ChemAxon
logS-3.2ALOGPS
pKa (Strongest Acidic)6.4ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area152.98 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity108.31 m³·mol⁻¹ChemAxon
Polarizability39.24 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+193.49132859911
AllCCS[M+H-H2O]+190.77532859911
AllCCS[M+Na]+196.71232859911
AllCCS[M+NH4]+195.99532859911
AllCCS[M-H]-193.23732859911
AllCCS[M+Na-2H]-193.14632859911
AllCCS[M+HCOO]-193.232859911
DeepCCS[M+H]+182.22630932474
DeepCCS[M-H]-179.83130932474
DeepCCS[M-2H]-213.03530932474
DeepCCS[M+Na]+188.13930932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pelargonidin 3-arabinoside 10V, Positive-QTOFsplash10-0udi-0100900000-329d32b4095b0460dbf72016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pelargonidin 3-arabinoside 20V, Positive-QTOFsplash10-0ue9-2504900000-806764417ac6eedeb4762016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pelargonidin 3-arabinoside 40V, Positive-QTOFsplash10-015a-9720000000-704a1306852c1a8509f32016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pelargonidin 3-arabinoside 10V, Negative-QTOFsplash10-0udi-1201900000-a9941913dfafb58e0c1e2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pelargonidin 3-arabinoside 20V, Negative-QTOFsplash10-0udj-2902800000-e95379d8402932da238f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pelargonidin 3-arabinoside 40V, Negative-QTOFsplash10-0f7o-8910000000-90c7367bf36d8bba49a02016-08-03Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB000031
KNApSAcK IDNot Available
Chemspider ID30780055
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available